Improved DNA sequencing technology is making reading genomes faster and cheaper every day. But modifying genes in microbes and other organisms still requires slow and painstaking effort. Now, researchers report that they've come up with a new way to modify the genomes of billions of microbes simultaneously and then finger the ones with the most interesting changes. Because the technique will likely work with most types of genomes, it could turbocharge efforts to engineer microbes to produce everything from novel therapeutic drugs to vast quantities of biofuels.
Modifying organisms' genetic material has become central to modern bioengineering. Scientists can introduce new genes and sets of genes, allowing organisms to make novel proteins, or alter existing genes to improve their activity in the cell. Once the genes are introduced and the cell begins reproducing, the copies can then be exposed to mutagens that cause random changes in their DNA, some of which can be useful. But in many cases, scientists would like to better direct these mutations to specific regions of the genome and make changes to several sites at the same time.
To do so, researchers led by synthetic biologist George Church of Harvard University came up with a new, high-speed technique called multiplexed automated genome engineering for targeting mutations. The researchers started by introducing three genes into an Escherichia coli bacterium that allowed it to make an antioxidant known as lycopene. They then identified 24 regions in the E. coli genome where they suspected that changes could improve the microbes' lycopene output. The researchers synthesized snippets of single stranded DNA known as oligos, each of which carried a unique mutation. They tailored each oligo to bind to one of the 24 target regions. Finally, the team subjected the target cells to a strong electric field. That temporarily poked holes in the cell membranes, allowing the oligos to diffuse inside and slip into the bacterial DNA.
The researchers report online this week in Nature that in just 3 days, they generated some 14.2 billion different mutations at the 24 sites. That led to an E. coli that produced five times more lycopene than did the original microbe. In the end, the researchers sequenced the genomes of the best lycopene producers to identify the exact mutations that boosted the output.
"The concept is nice," says James Liao, a bioengineer at the University of California, Los Angeles. He says that because the technique rapidly speeds and targets evolution, he anticipates using it in his own lab to find microbes that are more efficient at producing biofuels. However, Liao suspects the uses won't stop there. "It's a general method. It's up to the users to find the applications."